time integrators for molecular dynamics

Clicks: 34
ID: 144121
2013
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Abstract
This paper invites the reader to learn more about time integrators for Molecular Dynamics simulation through a simple MATLAB implementation. An overview of methods is provided from an algorithmic viewpoint that emphasizes long-time stability and finite-time dynamic accuracy. The given software simulates Langevin dynamics using an explicit, second-order (weakly) accurate integrator that exactly reproduces the Boltzmann-Gibbs density. This latter feature comes from adding a Metropolis acceptance-rejection step to the integrator. The paper discusses in detail the properties of the integrator. Since these properties do not rely on a specific form of a heat or pressure bath model, the given algorithm can be used to simulate other bath models including, e.g., the widely used v-rescale thermostat.
Reference Key
bou-rabee2013entropytime Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Nawaf Bou-Rabee
Journal European journal of medicinal chemistry
Year 2013
DOI
10.3390/e16010138
URL
http://www.mdpi.com/1099-4300/16/1/138
Keywords
weak accuracyscienceastrophysicsphysics

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